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Project Work Plan

Department of Interior USGS GE PES and ENP CESI

Fiscal Year 2007 Study Work Plan

Study Title: Effects of hydrological restoration on manatees: Integrating data and models for the Ten Thousand Islands and Everglades
Study Start Date: 1 December 2005   Study End Date: 30 September 2008
Web Sites: http://cars.er.usgs.gov/Manatees/manatees.html -
Location (Subregions, Counties, Park or Refuge): Total System - Ten Thousand Islands NWR, Collier County; Everglades National Park, Monroe County.
Funding Source: USGS Greater Everglades Priority Ecosystems Science (GE PES) and ENP Critical Ecosystems Studies Initiative (CESI)
Other Complementary Funding Source(s): We have potential complementary funding pending from FWS.
Funding History: Funding began FY06
Principal Investigators: Catherine Langtimm, Brad Stith, Eric Swain, James Reid, Daniel Slone
Study Personnel: Melinda Wolfert, Robert Renken, Susan Butler (USGS contract), Skip Snow (ENP), Terry Doyle (USFWS-TTINWR), Robert Dorazio (USGS), Eduardo Patino (USGS), Jeremy Decker (USGS).
Supporting Organizations: U.S. Fish and Wildlife Service - Ten Thousand Islands National Wildlife Refuge; National Park Service - Everglades National Park, Big Cypress National Preserve; Florida Fish and Wildlife Conservation Commission - Florida Marine Research Institute
Associated / Linked Studies: This study is an extension of the GE PES study "Predicting effects of hydrologic restoration on manatees along the southwest coast of Florida ", which focused on the TTI region. This extends the research to a larger region. (Sofia website: http://sofia.usgs.gov/projects/manatees/ ). Additional linkages to other studies/databases include TIME model, ATLSS model, and associated PES/CESI studies including "Southwest Florida Coastal and Wetland Systems Monitoring Project " (E. Patino) ( http://sofia.usgs.gov/projects/sys_monitor/ ).

Overview & Objectives: A significant population of the endangered West Indian manatee occurs in southwest Florida, throughout extensive estuarine and coastal areas within the Ten Thousand Islands (TTI; managed primarily by FWS) and Everglades National Park (ENP; managed by NPS). Planned restoration activities for the Everglades and Picayune Strand (an Acceler-8 project which discharges into TTI) may impact manatees by changing availability of freshwater for drinking, the quality and availability of seagrass forage, and the quality and availability of passive thermal basins used for refuge from lethal winter cold fronts. We expect changes in freshwater availability and forage to result in a shift in manatee distribution, which could necessitate new management actions to reduce human-manatee interactions. Restoration also could negatively impact important passive thermal refugia by increasing cold sheet flow during winter or disrupting haloclines that maintain warm bottom layers of salty water. Recent telemetry and aerial survey studies of manatees in TTI have revealed much about their use of this area: this project will extend the study into ENP, where manatees have not been intensively studied. To ascertain how restoration may affect the distribution and abundance of manatees in the region, an individual-based model has been under development, but completion of that model requires a hydrologic model for the rivers and estuaries affected by the accelerated Picayune Strand restoration. This study will provide integrated regional hydrologic models covering nearly the entire southwest coast below Naples, including portions of Picayune Strand and Big Cypress, providing much needed hydrologic modeling capabilities for evaluating restoration effects on coastal, estuarine, and freshwater ecosystems. This effort will enable us to model manatee response to restoration, and more adequately address science and management needs. Three Tasks (described in detail below) will be undertaken to develop the necessary components for this regional model: (TASK 1) Link the TIME hydrology model and the ATLSS manatee model to assess restoration effects in the Everglades and Picayune Strand, (TASK 2) Model changes to manatee thermal refugia due to hydrological restoration, (TASK 3) Design and implement a regional manatee monitoring program using aerial surveys and use robust statistical analysis techniques to estimate manatee distribution and abundance before restoration.

Specific Relevance to Major Unanswered Questions and Information Needs Identified:

This study will provide integrated regional hydrologic models covering nearly the entire southwest coast below Naples, including the Ten Thousand Islands National Wildlife Refuge, Collier Seminole State Park, Rookery Bay National Estuarine Research Reserve, as well as portions of Picayune Strand, Fakahatchee Strand Preserve State Park, and Big Cypress, providing much needed hydrologic modeling capabilities for evaluating restoration effects on coastal, estuarine, and freshwater ecosystems.

This study also will address two of the three overarching restoration questions in the DOI Science Plan. First, what actions will recover South Florida threatened and endangered species? The models produced will allow the effects of hydrologic modifications to the system to be evaluated in terms of the factors which affect manatees and other estuarine species sensitive to these factors. Second, what actions will improve the quantity, timing, and distribution of clean fresh water needed to restore the South Florida ecosystem? To determine the quantity, timing, and distribution needed in manatee habitats, a comparison of CERP restoration scenarios is needed. Additionally, the Tasks in this study will address three questions identified as priorities under Science Integration and Synthesis Questions for the FY06 and FY07 funding initiative:

  1. Synthesis of regional scale information and model development are needed that integrate and depict key factors of landscape change and their effects on the hydrology, biology, geology, and geography of the landscape, together with the identification of how policy, regulatory, and management strategies of national parks and refuges may influence these effects. Conceptual models and potential management options need to be developed with stakeholders. (TASK 1, TASK 2, TASK 3).
  2. Research to understand the impacts of restoration projects on hydrology, habitats, and wildlife within Ten Thousand Islands NWR and Everglades National Park. (TASK 1, TASK 2, TASK 3).
  3. Collection and synthesis of data for the verification and calibration of hydrologic and ecological models used for ecosystem assessment and restoration planning including those developed through the ATLSS program. (TASK 3).

Potential impacts: The endangered Florida manatee is a high priority species for management and recovery by USFWS and Florida's Fish and Wildlife Conservation Commission. In addition to concerns about the impact of restoration on manatees, the TTI/ENP region is the last major manatee habitat with minimal information on manatee population status. The results of this work will provide invaluable information to managers. The hydrology model provides data for the individual-based and landscape-based manatee models; defining the flow, salinity, and temperature information needed to model manatee movement and distribution. Comparisons of CERP restoration alternatives and associated alterations to the flow system in the hydrology model will show how habitat conditions change spatially and temporally. These hydrologic variables in turn will drive the individual-based model, which will project changes in manatee distribution and abundance across the region. Robust aerial surveys and analysis will provide the means to monitor impact as the restoration proceeds and provide independent data for validation of the model.

Status: Funded and initiated in FY06

Recent Products:

Swain, E., and B.M. Stith. 2006. Numerical modeling of heat and salinity transport for West Indian manatee habitats in southwest Florida. Greater Everglades Ecosystem Restoration Conference, 5-9 June 2006, Orlando Florida. [Presentation]

Stith, B.M., C.A. Langtimm, E. Swain, J.Reid. 2006. Linking a manatee individual-based model with the TIME hydrology model to assess restoration effects in the Everglades and Ten Thousand Islands. Greater Everglades Ecosystem Restoration Conference, 5-9 June 2006, Orlando Florida. [Presentation]

Langtimm, C.A., J. P. Reid, D. H. Slone, B. M. Stith, E. D. Swain, T. Doyle, R. Snow. 2006. Effects of hydrological restoration on manatees: A research program to integrate data, models and long-term monitoring across the Ten Thousand Islands and Everglades. Greater Everglades Ecosystem Restoration Conference, 5-9 June 2006, Orlando Florida. [Poster]

Langtimm, C. A., and E. D. Swain. 2006. PES/CESI 2006 work plan. Effects of hydrological restoration on manatees: Integrating data and models for the Ten Thousand Islands and Everglades http://sofia.usgs.gov/projects/workplans06/integrating_manatee.html

Metadata Record. Effects of hydrological restoration on manatees: Integrating data and models for the Ten Thousand Islands and Everglades.

SOFIA Project Page. Effects of hydrological restoration on manatees: Integrating data and models for the Ten Thousand Islands and Everglades. http://sofia.usgs.gov/projects/integrating_manatee/

Planned Products:

CESI 2006 annual progress report to Everglades National Park. 30 December 2006. Effects of hydrological restoration on manatees: Integrating data and models for the Ten Thousand Islands and Everglades

Swain, E., J. Decker, et al. Incorporation of heat transport in a linked surface-groundwater model. Publication in professional journal.

Stith, B. M. C. A. Langtimm. Estimation of manatee movement probabilities among habitat types for implementation into a spacially-explicit, individual-based model. Publication in professional journal.

Stith, B. M. Individual-based, spatially-explicit manatee model: application to the Everglades restoration. Publication in professional journal.

Stith, B. M., E. Swain, J. P. Reid, and C. A. Langtimm. January 2007. Presentation of progress and preliminary findings in FY2006. USFWS and CERP cooperators.

Final reports for each task to be completed by 30 Sep 2008.

Modeling results comparing the differences in manatee distribution for different restoration scenarios.

Datasets provided for use in the ATLSS viewer.

Planned direction in FY09 after this study ends: The results of the three Tasks of this study provide the groundwork for synthesizing a larger regional model. Task 1 may be extended into the Atlantic Coast to address manatee issues in that region. Task 2 may be extended to model thermal refugia across a broader region, providing more extensive capabilities for modeling winter temperatures for manatees and other cold-intolerant species (especially invasive species). In addition to information transfer to FWS and NPS, the PIs will coordinate with the FWS Florida Manatee Recovery and Implementation Team and its working groups (CERP Interagency Manatee Task Force, Manatee Population Status Working Group, Habitat Working Group, and Warm Water Task Force) to identify and develop research, policy, regulatory, and management strategies related to the results of this work.

WORK PLAN

Title of Task 1: Linking an individual-based manatee model with TIME and a new TTI hydrology model to assess CERP restoration effects on the Everglades and Ten Thousand Islands estuaries
Task Funding: USGS Greater Everglades Priority Ecosystems Science (GE PES) and ENP Critical Ecosystems Studies Initiative (CESI)
Task Leaders: Brad Stith and Eric Swain
Phone: (BMS) 352-264-3554, (EDS) 954-377-5925
FAX: (BMS) 352-374-8080, (EDS) 954-377-5901
Task Status: Active
Task priority: High
Time Frame for Task 1: FY06, FY07, FY08
Task Personnel: E. Swain, B. Stith, D. Slone, M. Wolfert, J. Reid, S. Butler, C. Langtimm, E. Patino, J. Decker

Task Summary and Objectives:

The major objective of this task is to integrate an individual-based manatee model with a hydrology model of the TTI estuaries, to evaluate how proposed restoration changes will affect the endangered manatee. In conjunction with the existing TIME model of the Everglades region, the new model will generate key hydrologic parameters that manatees respond to, including salinity and water temperature. The model will be applied in the TTI region mostly south of US41, with a few areas north of US41 such as the Acceler-8 Picayune Strand restoration area and the Big Cypress region, both important to manatees and identified as priorities in the DOI Science Plan. Field measurements of bathymetry, flow, salinity and temperature will be used to develop the TTI model. To help parameterize the modeled response of manatees to restoration, telemetry data will be collected and analyzed for manatees captured in ENP. Relationships between hydrologic conditions and variables such as manatee movement and habitat use will be incorporated into the manatee model. Coupling hydrological and individual-based manatee models will provide a useful tool for comparing the response of manatees to different hydrologic restoration scenarios.

Work to be undertaken during the proposal year and a description of the methods and procedures:

USGS hydrologists have developed a coupled surface- and ground-water hydrology application model (TIME), using the FTLOADDS model code (Swain and others, 2004), which can generate salinity and water temperature data for the major river systems, bays, and near-shore gulf region within ENP. During FY06, the heat transport capabilities of FTLOADDS were developed in the TIME area and the application to the Ten Thousand Islands (TTI) area created. The surface-water model component already had a simple heat-transport algorithm, and this was modified to function in the coastal wetlands environment. New capabilities include: 1) formulation configured to make use of local heat-flux data collected at field stations and coefficients based on this data; 2) effect of ground-water exchange and rainfall on heat content; and 3) effect of soil heat capacity on shallow surface-water. The heat transport capabilities have been shown to match field temperatures quite well and useful in defining the Manatee habitat zones. The FTLOADDS code incorporates salinity transport in both the ground-water and surface-water, and, with the ability to simulate heat transport, is able to model salinity and water temperature. Comparisons with manatee location data indicate the correlation between temperature and habitat. The work continues in FY07 with refinement of the TTI application. Water monitoring stations that log salinity and water temperature are distributed across much of the region and will be used for model calibration, as well as available point measurements of these parameters. As was done in the TIME area, data in the TTI area for areal variations in temperature are available from various sources, and the necessary solar radiation data exists at several locations. The refinement of the TTI model will expand the available locations for the comparison of the hydrologic model output and the manatee data. This analysis will continue for both the TIME and TTI areas, with a cross-correlation analysis of manatee migration patterns and the salinity/temperature patterns. Defined ecologic restoration scenarios will be simulated in both the TIME and TTI models to define the effects of changes in the model areas' inflows and flow distributions. Work will be completed on documenting the model construction and the heat-transport development.

In FY07, USGS manatee researchers will continue processing newly acquired telemetry data and complete various analyses needed to parameterize the individual-based manatee model. This includes data from manatees recently tagged in Whitewater Bay, as well as from 32 manatees tagged in TTI between June 2000 and June 2005, and miscellaneous tagged manatees that used the area (e.g. rescued animals). We are analyzing the telemetry data using several approaches reflecting the hierarchical structure of the individual-based model. To capture the variability of individual manatee behavior, we are analyzing manatee movement in a 3-level hierarchy. At the broadest scale, we are analyzing migratory behavior of manatees in the study area in response to major cold fronts. Our approach follows Deutsch et al. (2003), who identified several discrete categories of migratory behavior of manatees tagged on the east coast of Florida, ranging from long distance migrants to year-round residents. At the intermediate scale, we will continue developing seasonal home ranges based on new telemetry data collected during the dry, wet, and cold seasons using fixed kernel analysis with least-square cross validation. Resulting home ranges are providing measures of variability among individuals in home range characteristics, such as seasonal home range size and distance from critical resources. Accounting for this variability is important, since substantial heterogeneity in home ranges has been observed in tagged manatees on the east coast of Florida (Deutsch et al., 2003). The observed distribution of individual home ranges will be used to parameterize the home range allocation module of the individual-based model. At the finest scale, we will continue analyzing movements between different habitat zones during the three primary seasons (dry, wet, cold) using multi-state modeling. This new statistical approach implemented in programs MARK and M-SURGE (Williams et al. 2002) generates transition probabilities for movement between several broad habitat zones (e.g. offshore, bay, river) for each individual at a 6-hour time interval (reflecting the sampling interval of the Argos telemetry tags). The resulting distribution of Markovian probabilities are being used to parameterize the individual-based model, providing a useful technique for quantifying individual heterogeneity in movement behavior observed in tagged manatees as they make regular movements between offshore foraging zones and inshore zones with freshwater or thermal refugia (See Stith et al. 2004 and Reid et al. 2003 for further details on the observed movement patterns).

The manatee model is written in C++, allowing for the development of a flexible interface to read hydrologic output from the FTLOADDS model. The salinity and water temperature time-series output from FTLOADDS will be distributed across a network data structure to specific nodes representing destination sites for feeding, drinking, and sheltering from cold, with connections representing travel corridors. This network data structure allows directed manatee movements to be simulated in an efficient manner using well-known graph theory algorithms. The manatee model will increment through the seasonally changing hydrologic data, and manatees will respond to the availability of freshwater or warm water as they move across the network, using the parameters developed from the telemetry data. Large-scale migratory movements to winter home ranges are triggered by offshore water temperatures falling below 20 degrees Celsius on the network. Within a seasonal home range, transition probabilities obtained from the multi-state analysis are used to simulate the movement of manatees among ecological zones as a Markov chain process. To calibrate the model, simulations are run where each manatee is initially assigned to a home range drawn from the observed distribution of home ranges. As they move around the network seeking different resources, manatees are exposed to the simulated hydrologic conditions and experience positive or negative reinforcement (e.g. while transitioning up a river to find freshwater). Initially, manatees have no preferences for different parts of the network within their home range, but as they explore the network these preferences change based on a simple reinforcement model (see Sutton and Barto, 1998). During this learning phase, individuals shift their home ranges in response to positive and negative reinforcement. Once all individuals converge on stable home ranges, snapshots of the aggregate distribution of individuals will be generated and compared to aerial survey data collected for the same time period under similar hydrologic conditions. The aerial survey data will be subdivided, with one subset used to calibrate the model, and a holdout set to validate the model. Model calibration will primarily involve modifying the 2 or 3 parameters of the reinforcement model, which control the tradeoff between exploring less rewarding sites and maintaining site fidelity.

In FY07, we expect to have simulated hydrologic data from the TIME and TTI applications for different hydrologic restoration scenarios. These scenarios are designed to represent proposed system changes to support ecosystem objectives. At this time we will run the final set of restoration simulations with different hydrologic restoration scenarios and will compare the resulting manatee distribution for the dry, wet, and cold seasons. Comparison of the outcomes of these different restoration scenarios, with different quantities, timing, and distribution of freshwater flow into areas used by manatees will allow the effects of hydrologic modifications on manatees to be evaluated.

The results from the completion of this task will contribute to answering two of the overarching restoration questions in the DOI Science Plan: what actions will recover South Florida's threatened and endangered species; and what actions will improve the quantity, timing, and distribution of clean fresh water needed to restore habitats and species in the South Florida ecosystem? Additionally, the results will address two issues identified as priorities under Science Integration and Synthesis Questions for the FY06 and FY07 funding initiative: 1) the synthesis of regional scale information and model development to integrate and depict key factors of landscape change and their effects on the hydrology, biology, geology, and geography of the landscape; 2) understanding the impacts of restoration projects on hydrology, habitats, and wildlife on Ten Thousand Islands NWR.

FY08 work will involve the continued comparison and evaluation of the hydrologic and manatee information and the documentation of the results. Conclusions will include the effects of specific changes in the water management system on manatees and their habitats. A method of parameterizing locations as to manatee suitability based on hydrologic factors will be documented.

Specific Task Products

(1) Annual report to be completed by 30 Sep 2008. Report will contain: a) an analysis of the actual movement of tagged manatees, showing their movement patterns, travel corridors, home ranges, use of freshwater sites, foraging areas, winter refugia, and observed movements; b) results of the hydrologic model showing pre-restoration hydrological parameters relevant to manatee behavior; c) results of model calibration and validation using manatee aerial survey analyses; d) maps, graphs, and tables.

(2) Journal articles to be submitted for peer review in scientific journals will be completed as the various components of this task are completed. Manuscript preparation and publication may extend into or beyond FY08.

(3) Updates and reports on important findings will be conveyed to NPS, USFWS and the Manatee Recovery and Implementation Team as they become available. This will facilitate the identification and development of research, policy, regulatory, and management strategies relevant to manatees and restoration, and pave the way for the development of conceptual models and potential management options with stakeholders. This is one of the key issues identified by DOI for the FY06 and FY07 funding initiative.

Title of Task 2: Hydrologic modeling and manatee winter use patterns at passive thermal refuges
Task Funding: USGS Greater Everglades Priority Ecosystems Science (GE PES) and ENP Critical Ecosystems Studies Initiative (CESI)
Task Leader: Eric Swain, James Reid and Daniel Slone
Phone: (EDS) 954-377-5925, (JPR 352-2654-3546) (DHS 352-264-3551)
FAX: (EDS) 954-377-5901, (JPR, DHS) 352-374-8080
Task Status: Active
Task priority: Medium
Time Frame for Task 2: FY06, FY07, FY08
Task Personnel: E. Swain, E. Patino, J. Reid, D. Slone

Task Summary and Objectives:

Cold stress is a major source of winter mortality for manatees in TTI and ENP. Previous USGS research in TTI has shown that tagged manatees during cold periods spend more time inshore in canal systems that serve as passive thermal refugia (e.g. Port of the Islands basin in the Faka Union canal, Wooten's basin of the Tamiami canal, and Big Cypress Preserve Oasis Ranger Station canals). During much of the winter season, vertical profiles at these sites indicate a halocline of warmer salt water trapped below a cooler freshwater lens, resulting in a thermal inversion (Reid et al. 2004). The hydrological process producing this halocline and how restoration may disrupt its thermal properties is not well understood. The objectives of this Task are to evaluate the importance of these winter refugia to manatee over-wintering strategies in the region and to collaborate with USGS hydrologists to characterize and model the three-dimensional properties for several key aggregation sites used during winter by manatees in the TTI. This modeling effort will provide important information on the salinity and temperature regimes of canals critical to manatees and other cold-intolerant species, such as invasive, exotic fish species in south Florida. This study has significant implications for understanding passive thermal refuges used by manatees and other species state-wide.

Work to be undertaken during the proposal year and a description of the methods and procedures:

In FY07 we will continue field-data collection at Port of the Islands in support of parameterization of the three-dimensional model, including field measurements of salinity and temperature, along with high-resolution bathymetry of the basin to be simulated. Measurements of these relevant parameters at some locations also continue to be made by the USGS in cooperation with the South Florida Water Management District. These measurements are not at the specific manatee habitat locations, but are necessary for model boundaries and calibration. In order to get data at the habitat locations, boat-based measurements and data-logging probes will be used to obtain vertical profiles of salinity and temperature at strategic locations. Bathymetric measurements will be made manually with GPS reference from a boat, or by acoustic Doppler meter, providing crucial discharge information as well. A continuously recording salinity and temperature gage will continue to supplement existing continuous measurements in the area. A series of data logging temperature probes will continue to operate at Port of the Islands basin, Wooten's basin, and Big Cypress Preserve Oasis Ranger Station canals. These hourly records of temperatures at different depths, combined with similar data collected over the previous two winters, will complement other hydrologic measurements and provide a better understanding of annual variations.

Also in FY07, we will continue to characterize the manatee use of these passive thermal refuges and correlate with hydrologic findings at each site. Manatees have been tracked in the TTI as part of a study on manatee use patterns and freshwater flows within the region, which primarily focused on movements outside the winter season. Also, a smaller number of manatees initially tagged in the southern Everglades continue to be tracked in the TTI. Additional information collected during ground and aerial surveys at specific aggregation sites provide data on numbers of manatees present before, during, and after major cold fronts. The new aerial survey work initiated this fiscal year will provide additional information to identify and characterize passive thermal refuges. Collectively, tracking and survey data will help identify manatee movement patterns associated with winter cold fronts. These findings, integrated in manatee movement models, will be coupled with hydrologic models on basin temperature and salinity to better understand the dynamics of these sites as passive thermal refuges.

Development of a 3-D hydrological model will be initiated in FY07. The hydrologic numerical modeling effort will use key manatee aggregation sites in the TTI as representative sites for the region as a whole. These specific winter-use areas have been observed to be deeper portions of inland canals, which typically hold higher temperature water during periods of declining air and ambient water temperatures associated with winter cold fronts. Sufficient field data exists to define the important attributes; salinity, temperature, bathymetry, and flow. The results of the larger scale TTI model can also be used to define the boundaries of the manatee aggregation site. It is important to represent vertical variations in salinity and temperature. This can be done with a three-dimensional flow and transport code that allows for salinity and temperature transport with associated density variations. The model is the best way to confirm the theory that salinity stratification could maintain a temperature inversion, providing a warm area at the bottom for manatees. A 1 psu change in salinity induces a 0.71 kg/m3 change in water density, and a 1°C change in temperature induces a 0.22 kg/m3 change in water density. This means that for every degree Celsius warmer a lower layer is, a 0.31 psu increase in salinity would be needed to compensate for the buoyancy. A 1 psu stratified salinity layer below freshwater could be 3 degrees warmer than the surface. This would make a significant difference to the manatee; when water temperature drops below 20°C, manatees seek warmer water to avoid hypothermia. The flow regime through manatee aggregation areas may affect the vertical stratification of salinity and temperature, and the value of the refuge. In the Ten Thousand Island region, ecosystem restoration is to be implemented across the Southern Golden Glades Estates/Picayune Strand with effects to flows in manatee-use areas south of US41. This should route water flows away from the current Faka Union canal flowways, but may shift the freshwater -saltwater transition zone seaward, possibly reducing haloclines fed by saltwater intrusion. The Faka Union and Big Cypress canals provide both treatment and control sites for understanding winter aggregations and changes due to restoration. These criteria and the target temperature and salinity will be used in the optimization model to determine the best flow regime based on the available conceptualization.

FY08 work will include documentation of the 3-D model development and the effects of water deliveries on the vertical thermal stratification. These inflows will be tied in with the restoration scenarios developed in the larger-scale TTI model, so that the smaller scale effects can be delineated. The results from the completion of this task will contribute to answering two of the overarching restoration questions in the DOI Science Plan: what actions will recover South Florida's threatened and endangered species; and what actions will improve the quantity, timing, and distribution of clean fresh water needed to restore habitats and species in the South Florida ecosystem? Additionally, the results will address two issues identified as priorities under Science Integration and Synthesis Questions for the FY06 and FY07 funding initiative: 1) the synthesis of regional scale information and model development to integrate and depict key factors of landscape change and their effects on the hydrology, biology, geology, and geography of the landscape; 2) understanding the impacts of restoration projects on hydrology, habitats, and wildlife on Ten Thousand Islands NWR.

Specific Task Products:

(1) Hydrologic data and manatee observations collected from the FY06 winter will be compiled and summarized with available data from previous years. Data sets will be available for modeling efforts to be initiated in FY07.

(2) Final report to be completed by 30 September 2008. Report will contain: a) discussion of the field measurements and model development process, including calibration and verification; b) results of the hydrologic model indicating predictions of habitat suitability as a function of flow conditions; c) relationships for use in the larger-scale model to represent the basin as an internal boundary.

(3) Journal articles to be submitted for peer review in scientific journals will be completed as the various components of this task are completed. Some manuscript preparation and publication may extend beyond FY08.

(4) Updates and reports on important findings will be conveyed to NPS, USFWS and the Manatee Recovery and Implementation Team as they become available. This will facilitate the identification and development of research, policy, regulatory, and management strategies relevant to manatees and restoration, and pave the way for the development of conceptual models and potential management options with stakeholders. This is one of the key issues identified by DOI for the FY06 and FY07 funding initiative.

Title of Task 3: Development of a monitoring design and analysis for manatee aerial surveys, integrating Ten Thousand Islands with Everglades
Task Funding: USGS Greater Everglades Priority Ecosystems Science (GE PES) and ENP Critical Ecosystems Studies Initiative (CESI)
Task Leader: Catherine Langtimm
Phone: 508-335-3029
FAX: 508-867-8346
Task Status: Active in FY07
Task priority: High
Time Frame for Task 3: FY07 and FY08
Task Personnel: C. Langtimm (USGS), B. Stith (USGS), R. Dorazio (USGS), T. Doyle (USFWS-TTINWR), and R. Snow (NPS-ENP)

Task Summary and Objectives:

The three main objectives of this Task are: (1) provide an independent data set for validation of the predictive manatee/hydrology models, (2) develop a statistically robust means to document changes in manatee distributions in association with habitat variables incorporated in the manatee/hydrology models, and (3) develop and implement a regional manatee monitoring design for pre- and post-restoration assessments, integrating TTI with ENP. Development of the manatee individual-based model has focused on time-intensive telemetry studies of a relatively small number of manatees. Aerial surveys, however, offer the best opportunity from a cost-effective and scientifically robust perspective to monitor and document the population across the entire region, as well as to provide independent data for model validation. Site occupancy or abundance of manatees in different "patches " estimated from aerial surveys, may change over time due to restoration activities. Robust statistical analyses of survey data will be important to managers to assess such restoration effects, as well as to assess impact and recovery after natural disturbances, such as hurricanes, which periodically affect this area.

Work to be undertaken during the proposal year and a description of the methods and procedures:

The main body of work for this task will begin in FY07. A new class of capture-recapture statistical models to estimate habitat site occupancy rates when detection of a species is imperfect has successfully been applied to manatee aerial survey data from TTI. The technique explicitly models detection probability using repeated presence/absence surveys to provide unbiased estimates of the proportion of sites occupied by a species or population. Extensions of the model also allow modeling of variation in habitat occupancy rates as a function of site characteristics, time, and environmental variables (MacKenzie et al. 2002); the estimation of rate of change in site occupancy over time (MacKenzie et al. 2003); and the estimation of abundance from presence/absence data (Royle and Nichols 2003) or from spatially replicated counts (Royle 2004, Dorazio et al. 2005, Royle and Dorazio in review). Modifications of the current survey designs at TTI to better meet the requirements for analysis are under development. Site occupancy rate and abundance will be estimated within "patches " delineated in different zones (e.g. tidal rivers and canals, inshore bays, offshore shoals) used by manatees. In FY06, we will complete the current retrospective analysis of survey data in TTI, and in FY07 extend the research to ENP to develop the integrated monitoring program. USGS will collaborate with Park and Refuge biologists to modify the existing distribution survey routes and protocols into a common design. A small series of surveys will be flown to test the new design and flight logistics. In FY08, a complete series of survey flights will be conducted in both regions. The data from these flights will be analyzed for the pre-restoration assessment of site occupancy and abundance in association with key environmental variables in the individual-based models. These site occupancy estimates will be compared to the output of the individual-based model (Task 1) for model validation.

The results from the completion of this task will contribute to answering two of the overarching restoration questions in the DOI Science Plan: what actions will recover South Florida's threatened and endangered species; and what actions will improve the quantity, timing, and distribution of clean fresh water needed to restore habitats and species in the South Florida ecosystem? Additionally, the results will address three issues identified as priorities under Science Integration and Synthesis Questions for the FY06 and FY07 funding initiative: 1) the synthesis of regional scale information and model development to integrate and depict key factors of landscape change and their effects on the hydrology, biology, geology, and geography of the landscape; 2) understanding the impacts of restoration projects on hydrology, habitats, and wildlife on Ten Thousand Islands NWR; and 3) collection and synthesis of data for the verification and calibration of hydrologic and ecological models used for ecosystem assessment and restoration planning.

Specific Task Products:

(1) Report detailing the regional monitoring design, protocols, and methods for analysis, completed by 30 Sep 2008.

(2) Report describing the regional pre-restoration assessment of manatee distributions, completed by 2 February 2009.

(3) Datasets provided to modelers for validation analysis, as they become available.

(4) Journal articles to be submitted for peer review in scientific journals will be completed as the various components of this task are completed.

(5) Updates and reports on important findings will be conveyed to NPS, USFWS and the Manatee Recovery and Implementation Team as they become available. This will facilitate the identification and development of research, policy, regulatory, and management strategies relevant to manatees and restoration, and pave the way for the development of conceptual models and potential management options with stakeholders. This is one of the key issues identified by DOI for the FY06 and FY07 funding initiative.

LITERATURE CITED

Deutsch, C.J., Reid, J.P., Bonde, R.K., Easton, D.E., Kochman, H.I. and O'Shea, T.J., 2003. Seasonal movements, migratory behavior, and site fidelity of West Indian manatees along the Atlantic Coast of the United States: The Wildlife Society. Wildlife Monographs No. 151, 77 pp.

Dorazio, R. M., H. L. Jelks, and F. Jordan. 2005. Improving removal-based estimates of abundance by sampling a population of spatially distinct subpopulations. Biometrics 61, in press.

MacKenzie, D. I., J. D. Nichols, G. B. Lachman, S. Droege, J. A. Royle, and C. A. Langtimm. 2002. Estimating site occupancy rates when detection probabilities are less than one. Ecology 83:2248-2255.

MacKenzie, D. I., J. D. Nichols, J. E. Hines, M. G. Knutson, and A. B. Franklin. 2003. Estimating site occupancy, colonization, and local extinction when a species is detected imperfectly. Ecology 84:2200-2207.

Reid, J. P., S. M. Butler, D. E. Easton, and B. M. Stith. 2003. Movements and Habitat Requirements of Radio Tagged Manatees in Southwest Florida; Implications for Restoration Assessment. Poster Presentation. Proceedings of the Joint Conference on the Science and Restoration of the Greater Everglades and Florida Bay Ecosystem, April 13-18, 2003, Palm Harbor, Florida. Website: http://sofia.usgs.gov/geer/2003/posters/radiotrack/.

Reid, J. P., B. M. Stith, and S. M. Butler. 2004. Are Manatee Over-Wintering Strategies and Restoration Efforts Compatible in the Northwestern Everglades Region?. First National Conference on Ecosystem Restoration (NCER), Orlando, FL, December 6-10, 2004. Website: http://sofia.usgs.gov/publications/posters/manatee_winter/

Royle, J. A. and R. M. Dorazio. (In review). Hierarchical models of animal abundance and occurrence. Journal of Agricultural, Environmental, and Biological Statistics.

Stith, B., J. Reid, and S. Butler. 2003. Modeling manatee response to restoration in the Ten Thousand Islands and Everglades National Park. First National Conference on Ecosystem Restoration (NCER), Orlando, FL, December 6-10, 2004. Website http://sofia.usgs.gov/publications/posters/modelmanatee/.

Stith, B., J. Reid, S. Butler, T. Doyle, and C. Langtimm. 2004. Predicting the effects of hydrologic restoration on manatees along the southwest coast of Florida. USGS Fact sheet 2004-3137.

Sutton, R.S. and A.G. Barto. Reinforcement Learning. 1998. MIT Press, Cambridge, Mass. 322 pp.

Swain, E.D., Wolfert, M.A., Bales, J.D., and Goodwin, C.R., 2004, Two-dimensional hydrodynamic simulation of surface-water flow and transport to Florida Bay through the Southern Inland and Coastal Systems (SICS): USGS Water-Resources Investigations Report 03-4287, 56 p. plus 6 plates.

Royle, J. A. 2004. N-mixture models for estimating population size from spatially replicated counts. Biometrics 60:108-115.

Royle, J. A., and J. D. Nichols. 2003. Estimating abundance from repeated presence-absence data or point counts. Ecology 84:777-790.

Williams, B. K., J.D. Nichols, and M.J. Conroy. 2002. Analysis and Management of Animal Populations. Academic Press. N.Y. 835 pp.



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